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micropan (version 2.0)

Microbial Pan-Genome Analysis

Description

A collection of functions for computations and visualizations of microbial pan-genomes.

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Version

Install

install.packages('micropan')

Monthly Downloads

313

Version

2.0

License

GPL-2

Maintainer

Lars Snipen

Last Published

January 19th, 2020

Functions in micropan (2.0)

micropan

Microbial Pan-Genome Analysis

getAccessions

Collecting contig accession numbers

readHmmer

Reading results from a HMMER3 scan

rarefaction

Rarefaction curves for a pan-genome

geneWeights

Gene cluster weighting

panPca

Principal component analysis of a pan-matrix

hmmerCleanOverlap

Removing overlapping hits from HMMER3 scans

heaps

Heaps law estimate

panPrep

Preparing FASTA files for pan-genomics

xmpl

Data sets for use in examples

xzcompress

Compressing and uncompressing text files

fluidity

Computing genomic fluidity for a pan-genome

panMatrix

Computing the pan-matrix for a set of gene clusters

hmmerScan

Scanning a profile Hidden Markov Model database

isOrtholog

Identifies orthologs in gene clusters

distJaccard

Computing Jaccard distances between genomes

distManhattan

Computing Manhattan distances between genomes

bClust

Clustering sequences based on pairwise distances

entrezDownload

Downloading genome data

dClust

Clustering sequences based on domain sequence

chao

The Chao lower bound estimate of pan-genome size

bDist

Computes distances between sequences based on BLAST results

binomixEstimate

Binomial mixture model estimates

blastpAllAll

Making BLAST search all against all genomes